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Weird organisms emerge from the deep, dark biosphere

THE strange organisms that eke out a living deep beneath our feet are finally being revealed by genetics. Many of them are small, co-dependent and fuelled by mysterious sources of energy.

We know that billions of microorganisms inhabit the earth, the underground aquifers that supply our drinking water, and even the deep nether regions of Earth’s crust, far beneath the seabed. But we know nothing about what most of these microbes are and how they live. Some of them, in the so-called “dark energy biosphere”, are the deepest living organisms, somehow surviving hundreds of metres underground, far from the sun’s life-giving light.

Millions of microorganisms inhabit the deep regions of Earth’s crust. But we know nothing about them

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“We know there are microbes living down there, but we have no idea what they do,” says Beth Orcutt of the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine. “We want to go after them.”

At the Goldschmidt conference in Sacramento, California, last week, Orcutt and Jill Banfield of the University of California, Berkeley, presented separate detailed surveys of these microbes, revealing what kinds of organisms live in such strange habitats and offering tantalising hints about their lifestyles. It is our first close look at an utterly alien world.

Banfield is using a brute-force approach called metagenomics. Essentially, she sequences the genomes of every organism in a given water or soil sample en masse; an entire community at once. It’s a kind of genetic census, and gives a sense of the richness of an ecosystem and how its members interact.

Metagenomics has already been used to sequence people’s gut flora, and the geneticist Craig Venter famously tried to sequence the uncounted microbes living in the ocean. But sequencing the full genomes of dozens or hundreds of species in one hit has proved challenging, so studies tend to focus on simple communities with relatively few species, or to settle for random chunks of DNA rather than complete genomes (Science, doi.org/s7m).

To solve this problem, Banfield is using sophisticated algorithms to digitally reassemble snippets of DNA into entire genomes. Her team has used this method to identify the microbes living in an aquifer near the Colorado River in Rifle, Colorado. They say they can now reliably get complete genomes from hundreds of organisms in one go, including rare ones that make up less than 0.1 per cent of the ecosystem.

“People have wanted to do that for ages,” says Orcutt. “Whatever computational approach they are using is revolutionary.”

The analysis has revealed some known microbes and many completely unstudied ones. Many of these mystery microbes are very small cells, with small genomes laced with unfamiliar genes. “Fifty per cent of the genes in these genomes have no known function,” says Banfield – an unusually high proportion.

Some of the microbes seem to lack a metabolism, so cannot feed themselves and may be reliant on other species for survival. As a result, they could never be grown in isolation in the lab, which helps explain why they have never been seen before.

Banfield has now used the DNA sequences to draw a family tree of all the microbes her team found in the aquifer. They found lots of completely unknown organisms, unrelated to anything that has ever been grown in a lab. All of these cryptic organisms clumped into one branch of the family tree.

Meanwhile, Orcutt is focusing not on aquifers but on hidden rivers flowing deep beneath the seabed, through cracks in the Earth’s crust. These channels may connect seemingly separate parts of the underworld.

To access them, she uses boreholes that have been drilled into the Juan de Fuca ridge in the north-eastern Pacific, where the Pacific plate dives beneath the North American plate.

The boreholes have been in place since 2010, sealed off at the top. In 2013, Orcutt’s team used a remotely operated underwater vehicle to collect water from observatories attached to the boreholes (pictured). This water should all have seeped up from the subsurface rivers below, rather than washing in from the ocean above. “These are probably the most pristine samples we’ve ever got from the deep marine biosphere,” says Orcutt.

Rather than sequencing all the microbes at once, Orcutt’s team picked out individual cells, broke them open, then collected and sequenced their DNA. Like Banfield, they found many organisms new to science.

Orcutt says the first question is how they survive. Their genes suggest they consume methane, which by itself is not surprising, as many other microbes use this as a source of energy. But earlier studies found hardly any methane beneath the Juan de Fuca ridge, says Orcutt.

We already knew that life in the deep subsurface is sparse. It may be that what does survive down there is scraping by on a larder that is virtually bare, effectively pushing at life’s lower limits.

This article appeared in print under the headline “Light cast on deep, dark biosphere”